[BiO BB] TopMatch /3D database interface

Mike Marchywka marchywka at hotmail.com
Sun Apr 20 09:19:54 EDT 2008

Apparently your QCOPS link below is for a structure navigator that requires flash.
I guess I'm looking for something like the result here,


( without even wanting the BLAST results ) but I want a text output to feed to other programs. 

Can I somehow post a pdb file to your server and get back a (text) list of molecules with
similarly shaped and colored ( by atoms that make up the cavity walls ) cavities?

This relates to my previous series of posts on the need for an API as opposed to just a human web interface.
I may want to use scripts or automated processes to sort through many candidates
before using an interactive navigator.

I was trying to figure out what databases exist that contain simplified shape and environment information
on cavities or surfaces for finding "accidental" ( without any obvious sequence homology) matches or near
matches of function.  You did mention things like conformations or modifications that distort the shape.
Obviously, you would like to find things that are close but not exact and try to figure out what implications
these may have for function. 


> Date: Wed, 2 Apr 2008 10:52:07 +0200
> From: markii at came.sbg.ac.at
> Indeed, the structural similarity of dehydrosqualene synthase (PDB codes: 2zco, 2zcp, 2zcq, 2zcr, 2czs) and humane squalene synthase (PDB codes 1ezf) is striking in the view of their low sequence identity. TopMatch-web yields an RMS of 3.5A and a sequence identity of 11% if the respective chains A are compared.
> Talking about finding such similarities: one tool that is really helpful for this task is the qCOPS web service (some advertising again ;-) at
> http://navi.services.came.sbg.ac.at/bin/qCOPS.html
> For further information on qCOPS, see
> Sippl et al.
> A Discrete View on Fold Space
> Bioinformatics, 24, pp. 870-871 (2008)
> (Open Access: http://bioinformatics.oxfordjournals.org/cgi/reprint/btn020?ijkey=7zgnEsdKQIEfrN7&keytype=ref)
> Best regards,
> -Markus
> On Die, 01 Apr 2008, Mike Marchywka wrote:
>> http://www.nature.com/nrd/journal/v7/n4/full/nrd2554.html
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